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- PDB-1bm9: REPLICATION TERMINATOR PROTEIN FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 1bm9
TitleREPLICATION TERMINATOR PROTEIN FROM BACILLUS SUBTILIS
ComponentsREPLICATION TERMINATOR PROTEIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / CONTRAHELICASE
Function / homology
Function and homology information


DNA replication termination / DNA binding
Similarity search - Function
Replication terminator protein / Replication terminator protein / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Replication termination protein / Replication termination protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsBussiere, D.E. / Bastia, D. / White, S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: Crystal structure of the replication terminator protein from B. subtilis at 2.6 A.
Authors: Bussiere, D.E. / Bastia, D. / White, S.W.
History
DepositionJul 29, 1998Processing site: BNL
Revision 1.0Jan 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REPLICATION TERMINATOR PROTEIN
B: REPLICATION TERMINATOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,0942
Polymers29,0942
Non-polymers00
Water3,117173
1
A: REPLICATION TERMINATOR PROTEIN

A: REPLICATION TERMINATOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,0942
Polymers29,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3080 Å2
ΔGint-25 kcal/mol
Surface area13850 Å2
MethodPISA, PQS
2
B: REPLICATION TERMINATOR PROTEIN

B: REPLICATION TERMINATOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,0942
Polymers29,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area3170 Å2
ΔGint-28 kcal/mol
Surface area13810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.191, 52.686, 70.583
Angle α, β, γ (deg.)90.00, 90.52, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.1813, 0.1268, 0.9752), (-0.0021, 0.9916, -0.1294), (-0.9834, -0.0255, -0.1795)
Vector: -29.317, -13.241, 86.5338)

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Components

#1: Protein REPLICATION TERMINATOR PROTEIN / RTP / TER


Mass: 14547.163 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Cell line: BL21 / Gene: RTP / Plasmid: PET-13A / Species (production host): Escherichia coli / Gene (production host): RTP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P68732, UniProt: P0CI76*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS DNA-BINDING PROTEIN IS A DIMER OF TWO WINGED HELIX MOTIFS JOINED BY AN ANTIPARALLEL COILED- ...THIS DNA-BINDING PROTEIN IS A DIMER OF TWO WINGED HELIX MOTIFS JOINED BY AN ANTIPARALLEL COILED-COIL AT THE C-TERMINUS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 50 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(w/v)PEG20001reservoir
20.125 MMES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1994 / Details: CRYSTAL/COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. obs: 16299 / % possible obs: 84.9 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.1 / Net I/σ(I): 7
Reflection shellResolution: 2→2.2 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 2 / Rsym value: 0.2 / % possible all: 70
Reflection shell
*PLUS
% possible obs: 70 %

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Processing

Software
NameVersionClassification
PHASESphasing
CNS0.3refinement
R-AXISdata reduction
R-AXISdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 501847.89 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1263 7.7 %RANDOM
Rwork0.206 ---
obs0.206 16299 84.9 %-
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.71 Å20 Å20.28 Å2
2---4.51 Å20 Å2
3----0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 0 173 2183
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.47
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 165 8.4 %
Rwork0.299 1808 -
obs--61.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.47

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